fmriprep
a BIDS app that runs a standardized and reproducible preprocessing pipeline on structural and functional MRI data
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a BIDS app that runs a standardized and reproducible preprocessing pipeline on structural and functional MRI data
Last updated
Was this helpful?
We keep up-to-date Singularity images for fmriprep
for the community. (Look in /oscar/data/bnc/simgs/nipreps/
to see which versions we currently have available.) In order to run fmriprep
on Oscar, you'll need to write a batch script. Here is an example:
The first part of the script configures the variables (e.g., number of cores, memory, etc) for your JOB. Make sure to update the email address if you'd like to get email updates about your job.
The second part invokes fmriprep
singularity image. Keep in mind the following considerations:
Singularity containers run as your user, and therefore should have the same read/write permissions as your local user in the cluster
Singularity containers only share $HOME
with the Oscar file system. Therefore, any other location that we want to read and write to/from, needs to be specified using the --bind hostfolder:containerfolder
input. This includes any directory in your home directory that is a symbolic link. For instance $HOME/data
usually points to /oscar/data/<group>
in that case we must bind /oscar/data/<group>
You must specify the location inside the container of the FreeSurfer license.
âś‹ Troubleshooting:
fmriprep
may fail for many reasons. Here are few tips:
Freesurfer is often difficult to get to completion, if it helps troubleshooting, you can turn FreeSurfer reconstruction off by adding the flag --fs-no-reconall
⚠️ At least as of fmriprep version 23.1.3, susceptibility distortion correction performs very poorly if you supply phase difference field maps like we have in the demodat dataset, actually making distortion worse. Distortion correction performance is much better with the 20.2.7 LTS version of fmriprep, which we also have available on Oscar.
To build the image, you can run:
For more information about managing your job, see the
Familiarize yourself with the inputs and don't hesitate to ask the developers questions. Good places to look/ask for help are their GitHub issues and the
If you wish to use a version not available under /oscar/data/bnc/simg/nipreps
, you'll need to build the image. Singularity images can be large, therefore consider using a place with sufficient quota and changing the default location singularity uses to cache these files. Please see .
Replace version
in the command above with the desired docker tag. You can find the latest tags of fmriprep